PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells-Dataset
Cite this dataset
Chang, Mau-Sun et al. (2023). PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells-Dataset [Dataset]. Dryad. https://doi.org/10.5061/dryad.cjsxksnb5
Abstract
PHRF1 is an E3 ligase that promotes TGF-B signaling by ubiquitinating a homeodomain repressor TG-interacting factor (TGIF). The suppression of PHRF1 activity by PML-RAR facilitates the progression of acute promyelocytic leukemia (APL). PHRF1 also contributes to non-homologous end-joining in response to DNA damage by linking H3K36me3 and NBS1 with DNA repair machinery. However, its role in class switch recombination (CSR) is not well understood. In this study, we report the importance of PHRF1 in IgA switching in CH12F3-2A cells and CD19-Cre mice. Our studies revealed that Crispr-Cas9 mediated PHRF1 knockout and shRNA-silenced CH12F3-2A cells reduced IgA production, as well as decreased the amounts of PARP1, NELF-A, and NELF-D. The introduction of PARP1 could partially restore IgA production in PHRF1 knockout cells. Intriguingly, IgA, as well as IgG1, IgG2a, and IgG3, switchings were not significantly decreased in PHRF1 deficient splenic B lymphocytes isolated from CD19-Cre mice. The levels of PARP1 and NELF-D were not decreased in PHRF1-depleted primary splenic B cells. Overall, our findings suggest that PHRF1 may modulate IgA switching in CH12F3-2A cells.
README: Title of Dataset:
PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells-Dataset
Description of the Data and file structure
The file is the result of RNA-seq analysis in "PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells". The samples include normal CH12F3-2A cells and PHRF1 gene knockout CH12F3-2A cells. RNA was extracted and sequenced by next-generation sequence. The raw data is analyzed with the bioinformatic tool.
File Cr_wt_Comparison_CH12F3_FC_over_2 is RNA seq data from 3 normal CH12F3-2A cells (WT) and 3 PHRF1 gene knockout CH12F3-2A cells (Cr). The raw data is analyzed with CLC Genomics Workbench v10. The comparison report contains the following information:
Name: Gene name.
Chromosome: Chromosome of gene
Region: Region of gene
Gene length: The length of gene.
Exon length: The total length of exon.
Exon: The number of exon.
Gene ID: Gene ID
Gene Description: Description of gene
EntrezGene ID: The gene ID in NCBI
Biotype: The type of gene.
Transcripts annotated: The number of transcripts
GO Biological Process: Biological process of GO
GO Cellular Component: Cellular component of GO
GO Molecular Function: Molecular function of GO
KEGG Pathway: KEGG pathway of gene
Target-based of Drugs from KEGG (Human): Target-based of Drugs with genes from KEGG in human.
Fold Change: For a two-group experiment the 'Fold Change' tells you how many times bigger the mean expression value in group 2 is relative to that of group 1. If the mean expression value in group 2 is bigger than that in group 1 this value is the mean expression value in group 2 divided by that in group 1. If the mean expression value in group 2 is smaller than that in group 1 the fold change is the mean expression value in group 1 divided by that in group 2 with a negative sign. Thus, if the mean expression levels in group 1 and group 2 are 10 and 50 respectively, the fold change is 5, and if the and if the mean expression levels in group 1 and group 2 are 50 and 10 respectively, the fold change is -5. For experiments with more than two groups, the 'Fold Change' column contains the ratio of the maximum of the mean expression values of the groups to the minimum of the mean expression values of the groups, multiplied by -1 if the group with the maximum mean expression value occurs before the group with the minimum mean expression value (with the ordering: group 1, group 2, ...).
Adjust Pvalue (Benjamini-Hochberg): Adjust p-value from DESeq2 (R package: v. 1.30.1). The smaller, the more significant FPKM. This is the expression value measured in FPKM.
Mean. The mean of FPKM
Total exon fragments: Total exon fragments of gene
File KEGG Pathway_list is Pathway enrichment Analysis report. RNA-Seq data is analyed by KEGG Orthology system -Pathway and Gene -orthology group http://www.genome.jp/kegg/ko.html (version: 2016/05/24). The report contains the following information:
PathwayID: Pathway ID in KEGG database.
Pathways description: Description of pathway.
Number of DEGs with pathway annotation: Genes involved in the term
Number of DEGs with pathway annotation %: percentage of the gene involved in the term
Up regulated: Number of the up regulated genes
Down regulated: Number of the down regulated genes
Number of All genes with pathway annotation: All Genes involved in the term
Number of All genes with pathway annotation %: Percentage of all Genes involved in the term
P-Value: Modified Fisher Extact P-Value, EASE Score. (The smaller, the more enriched.)
Q-value: Q-value by q-value (R package: v1.38.0). Ref1: Bass JDSwcfAJ, Dabney A and Robinson D (2015). qvalue: Q-value estimation for false discovery rate control. Ref2: https://bioconductor.org/packages/release/bioc/html/qvalue.html
Bonferroni: To globally correct enrichment P-values to control (Bonferroni correction)
Benjamini: To globally correct enrichment P-values to control (Benjamini & Hochberg’s)
FDR: To globally correct enrichment P-values to control (False discovery rate)
Gene(Up): Gene list of up regulated genes
Gene(Down): Gene list of down regulated genes
Sharing/access Information
Links to other publicly accessible locations of the data: https://doi.org/10.5061/dryad.cjsxksnb5
Was data derived from another source?
No
Methods
The file is the result of RNA-seq analysis in "PHRF1 promotes the class switch recombination of IgA in CH12F3-2A cells". The samples include normal CH12F3-2A cells and PHRF1 gene knockout CH12F3-2A cells. RNA was extracted and sequenced by next-generation sequence. The raw data is analyzed with KEGG pathway enricment.
Usage notes
The file is compatible with Microsoft Excel.
Funding
National Science and Technology Council